RELION

RELION - REgularised LIkelihood OptimisatioN - is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy (cryo-EM). It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology.

To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark relion.

Test Created

13 January 2021

Test Maintainer

Michael Larabel 

Test Type

Processor

Average Install Time

8 Minutes, 28 Seconds

Average Run Time

1 Hour, 16 Minutes, 9 Seconds

Test Dependencies

OpenMPI + FFTW + Git + CMake + TIFF Image + C/C++ Compiler Toolchain

Supported Platforms


Public Result UploadsReported Installs*Test Completions*OpenBenchmarking.orgEventsRELION Popularity Statisticspts/relion2021.012021.022021.032021.042021.05306090120150
* Data based on those opting to upload their test results to OpenBenchmarking.org and users enabling the opt-in anonymous statistics reporting while running benchmarks from an Internet-connected platform.
Data current as of Fri, 07 May 2021 23:52:07 GMT.

Revision History

pts/relion-1.0.1   [View Source]   Wed, 13 Jan 2021 16:14:18 GMT
Build without the GUI to avoid fltk dependency and since GUI isn't used anyway...

pts/relion-1.0.0   [View Source]   Wed, 13 Jan 2021 10:31:35 GMT
Initial commit of RELION Cryo-EM benchmarks.

Suites Using This Test

HPC - High Performance Computing


Performance Metrics

Analyze Test Configuration:

RELION 3.1.1

Test: Basic - Device: CPU

OpenBenchmarking.org metrics for this test profile configuration based on 177 public results since 13 January 2021 with the latest data as of 3 May 2021.

Below is an overview of the generalized performance for components where there is sufficient statistically significant data based upon user-uploaded results. It is important to keep in mind particularly in the Linux/open-source space there can be vastly different OS configurations, with this overview intended to offer just general guidance as to the performance expectations.

Component
Percentile Rank
# Matching Public Results
Seconds (Average)
Mid-Tier
75th
> 386
70th
5
468 +/- 5
67th
5
498 +/- 3
55th
5
572 +/- 3
Median
50th
655
47th
5
758 +/- 3
38th
7
1247 +/- 5
29th
3
1601 +/- 4
Low-Tier
25th
> 1635
22nd
4
1806 +/- 3
13th
4
2212 +/- 279
9th
6
2441 +/- 14
6th
3
3054 +/- 58
3rd
3
4674 +/- 6
OpenBenchmarking.orgDistribution Of Public Results - Test: Basic - Device: CPU177 Results Range From 234 To 7536 Seconds2343815286758229691116126314101557170418511998214522922439258627332880302731743321346836153762390940564203435044974644479149385085523253795526567358205967611462616408655567026849699671437290743775841020304050

Based on OpenBenchmarking.org data, the selected test / test configuration (RELION 3.1.1 - Test: Basic - Device: CPU) has an average run-time of 53 minutes. By default this test profile is set to run at least 3 times but may increase if the standard deviation exceeds pre-defined defaults or other calculations deem additional runs necessary for greater statistical accuracy of the result.

OpenBenchmarking.orgMinutesTime Required To Complete BenchmarkTest: Basic - Device: CPURun-Time4080120160200Min: 4 / Avg: 52.01 / Max: 234

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.3%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsTest: Basic - Device: CPUDeviation246810Min: 0 / Avg: 0.34 / Max: 2

Notable Instruction Set Usage

Notable instruction set extensions supported by this test, based on an automatic analysis by the Phoronix Test Suite / OpenBenchmarking.org analytics engine.

Instruction Set
Support
Instructions Detected
SSE2 (SSE2)
Used by default on supported hardware.
 
MOVDQU COMISD MOVAPD XORPD MULSD ANDPD CVTSI2SD DIVSD ADDSD SUBSD MOVDQA PUNPCKLQDQ MOVD PSHUFD MOVUPD SHUFPD UNPCKHPD UNPCKLPD MULPD UCOMISD CVTTSD2SI CVTSS2SD SQRTSD ANDNPD CMPNLESD ORPD CVTPS2PD CVTDQ2PD CMPLTPD ADDPD PMULUDQ PSRLDQ CMPLESD SUBPD MOVHPD PSUBQ PADDQ MINSD MOVLPD CMPLEPD CVTPD2PS CVTSD2SS MAXSD DIVPD CMPNLTSD CMPLTSD CVTDQ2PS
Requires passing a supported compiler/build flag (verified with targets: sandybridge, skylake, tigerlake, cascadelake, sapphirerapids, alderlake, znver2, znver3).
Found on Intel processors since Sandy Bridge (2011).
Found on AMD processors since Bulldozer (2011).

 
VZEROUPPER VEXTRACTF128 VINSERTF128 VPERM2F128 VPERMILPD VBROADCASTSD VBROADCASTSS
Requires passing a supported compiler/build flag (verified with targets: skylake, tigerlake, cascadelake, sapphirerapids, alderlake, znver2, znver3).
Found on Intel processors since Haswell (2013).
Found on AMD processors since Excavator (2016).

 
VEXTRACTI128 VPERMQ VPERMPD VINSERTI128 VPBROADCASTD VPBROADCASTQ VPERM2I128 VPMASKMOVD VPBROADCASTW VPBROADCASTB
FMA (FMA)
Requires passing a supported compiler/build flag (verified with targets: skylake, tigerlake, cascadelake, sapphirerapids, alderlake, znver2, znver3).
Found on Intel processors since Haswell (2013).
Found on AMD processors since Bulldozer (2011).

 
VFMADD231SD VFMADD132SD VFNMADD132SD VFMSUB132PD VFMADD132PD VFNMADD231SD VFMADD231PD VFMSUB231SD VFMSUB132SD VFMADD213SD VFNMADD213SD VFNMSUB132SD VFMSUB213SD VFMADD213PD VFMSUB231PD VFNMSUB231SD VFNMADD213PD VFNMADD132PD VFMADD132SS VFNMADD132SS VFMADD231SS
The test / benchmark does honor compiler flag changes.
Last automated analysis: 31 January 2021

This test profile binary relies on the shared libraries libmpi.so.40, libdl.so.2, libtiff.so.5, libfftw3f.so.3, libfftw3.so.3, libpng16.so.16, libm.so.6, libgomp.so.1, libpthread.so.0, libc.so.6, libopen-rte.so.40, libopen-pal.so.40, libhwloc.so.15, libwebp.so.6, libzstd.so.1, liblzma.so.5, libjbig.so.0, libjpeg.so.8, libz.so.1, libevent-2.1.so.7, libutil.so.1, libudev.so.1.

Recent Test Results

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1 System - 732 Benchmark Results

2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998

Ubuntu 20.04 - 5.11.6-051106-generic - GNOME Shell 3.36.4

4 Systems - 179 Benchmark Results

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Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4

3 Systems - 179 Benchmark Results

AMD Ryzen 5 5600X 6-Core - ASRock X570 Taichi - AMD Starship

Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4

3 Systems - 179 Benchmark Results

Intel Core i5-11600K - ASUS ROG MAXIMUS XIII HERO - Intel Device 43ef

Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4

1 System - 179 Benchmark Results

Intel Core i5-11600K - ASUS ROG MAXIMUS XIII HERO - Intel Device 43ef

Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4

2 Systems - 255 Benchmark Results

AMD EPYC 75F3 32-Core - AMD DAYTONA_X - AMD Starship

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1 System - 255 Benchmark Results

2 x AMD EPYC 7763 64-Core - AMD DAYTONA_X - AMD Starship

Ubuntu 20.04 - 5.11.6-051106-generic - GNOME Shell 3.36.4

4 Systems - 290 Benchmark Results

2 x AMD EPYC 7742 64-Core - Supermicro H11DSi-NT v2.00 - AMD Starship

Ubuntu 20.04 - 5.8.0-44-generic - X Server 1.20.8

3 Systems - 74 Benchmark Results

Intel Core i5-10600K - ASUS PRIME Z490M-PLUS - Intel Comet Lake PCH

Ubuntu 20.04 - 5.9.0-050900daily20201012-generic - GNOME Shell 3.36.4

6 Systems - 78 Benchmark Results

AMD Ryzen Threadripper 2990WX 32-Core - ASUS ROG ZENITH EXTREME - AMD 17h

Ubuntu 20.10 - 5.8.0-34-generic - GNOME Shell 3.38.1

3 Systems - 376 Benchmark Results

2 x AMD EPYC 7F72 24-Core - Supermicro H11DSi-NT v2.00 - AMD Starship

Ubuntu 20.10 - 5.11.0-rc4-max-boost-inv-patch - GNOME Shell 3.38.1

Most Popular Test Results

OpenBenchmarking.org Results Compare

3 Systems - 32 Benchmark Results

2 x Intel Xeon Gold 5220R - TYAN S7106 - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.04 - 5.9.0-050900rc6-generic - GNOME Shell 3.36.4

4 Systems - 9 Benchmark Results

AMD Ryzen 9 3900XT 12-Core - MSI MEG X570 GODLIKE - AMD Starship

Ubuntu 20.10 - 5.11.0-rc1-phx - GNOME Shell 3.38.1

3 Systems - 34 Benchmark Results

Intel Xeon E3-1235L v5 - ASRockRack C236M WS - Intel Xeon E3-1200 v5

Ubuntu 20.04 - 5.8.0-050800-generic - GNOME Shell 3.36.4

3 Systems - 58 Benchmark Results

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Ubuntu 20.04 - 5.9.0-050900rc6daily20200921-generic - GNOME Shell 3.36.4

4 Systems - 179 Benchmark Results

AMD Ryzen 5 5600X 6-Core - ASRock X570 Taichi - AMD Starship

Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4

3 Systems - 18 Benchmark Results

Intel Core i9-10980XE - ASRock X299 Steel Legend - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.04 - 5.11.0-rc2-phx - GNOME Shell 3.36.4

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Ubuntu 20.10 - 5.11.0-rc2-phx - GNOME Shell 3.38.1

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